A novel putative miRNA target enhancer signal

PLoS ONE

Volumn 4, Issue 7, 2009, Pages

  Schmidt, Thorsten ^a   Mewes, Hans Werner ^a,b   Stümpflen, Volker ^a  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA;

ARTICLE; CONTROLLED STUDY; DOWNSTREAM PROCESSING; ENHANCER REGION; GC RICH SEQUENCE; HUMAN; MOLECULAR BIOLOGY; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN RNA BINDING; PROTEIN TARGETING; RNA STABILITY; RNA STRUCTURE; RNA TRANSCRIPTION; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; 3' UNTRANSLATED REGION; GENETICS;

3' UNTRANSLATED REGIONS; ENHANCER ELEMENTS, GENETIC; HUMANS; MICRORNAS;

EID: 68149106153     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0006473     Document Type: Article

References (39)

1. Ambros V (2004) The functions of animal microRNAs. Nature 431: 350-355.
2. Baulcombe D (2004) RNA silencing in plants. Nature 431: 356-363.
3. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
4. Griffiths-Jones S (2006) miRBase: the microRNA sequence database. Methods Mol Biol 342: 129-138.
5. Didiano D, Hobert O (2006) Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions. Nat Struct Mol Biol 13: 849-851.
6. Didiano D, Hobert O (2008) Molecular architecture of a miRNA-regulated 3′ UTR. Rna 14: 1297-1317.
7. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115: 787-798.
8. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.
9. John B, Enright AJ, Aravin A, Tuschl T, Sander C, et al. (2004) Human MicroRNA targets. PLoS Biol 2: e363.
10. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, et al. (2005) Combinatorial microRNA target predictions. Nat Genet 37: 495-500.
11. Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, et al. (2006) A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126: 1203-1217.
12. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39: 1278-1284.
13. Yousef M, Jung S, Kossenkov AV, Showe LC, Showe MK (2007) Naive Bayes for microRNA target predictions-machine learning for microRNA targets. Bioinformatics 23: 2987-2992.
14. Rajewsky N (2006) L(ou)sy miRNA targets? Nat Struct Mol Biol 13: 754-755.
15. Carthew RW (2006) Gene regulation by microRNAs. Curr Opin Genet Dev 16: 203-208.
16. Stefani G, Slack FJ (2008) Small non-coding RNAs in animal development. Nat Rev Mol Cell Biol 9: 219-230.
17. Vella MC, Choi EY, Lin SY, Reinert K, Slack FJ (2004) The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3′UTR. Genes Dev 18: 132-137.
18. Nolde MJ, Saka N, Reinert KL, Slack FJ (2007) The Caenorhabditis elegans pumilio homolog, puf-9, is required for the 3′UTR-mediated repression of the let-7 microRNA target gene, hbl-1. Dev Biol 305: 551-563.
19. Kedde M, Strasser MJ, Boldajipour B, Vrielink JA, Slanchev K, et al. (2007) RNA-binding protein Dnd1 inhibits microRNA access to target mRNA. Cell 131: 1273-1286.
20. Ketting RF (2007) A dead end for microRNAs. Cell 131: 1226-1227.
21. Sethupathy P, Corda B, Hatzigeorgiou AG (2006) TarBase: A comprehensive database of experimentally supported animal microRNA targets. Rna 12: 192-197.
22. Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36.
23. Bailey TL, Williams N, Misleh C, Li WW (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34: W369-373.
24. Roepcke S, Grossmann S, Rahmann S, Vingron M (2005) T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Res 33: W438-441.
25. Wingender E (2004) TRANSFAC, TRANSPATH and CYTOMER as starting points for an ontology of regulatory networks. In Silico Biol 4: 55-61.
26. Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B (2004) JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 32: D91-94.
27. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, et al. (2005) Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434: 338-345.
28. Lee JY, Yeh I, Park JY, Tian B (2007) PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res 35: D165-168.
29. Bailey TL, Gribskov M (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14: 48-54.
30. Rajewsky N (2006) microRNA target predictions in animals. Nat Genet 38 Suppl: S8-13.
31. Ding L, Han M (2007) GW182 family proteins are crucial for microRNA-mediated gene silencing. Trends Cell Biol 17: 411-416.
32. Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, et al. (2006) The UCSC Known Genes. Bioinformatics 22: 1036-1046.
33. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, et al. (2008) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 36: D13-21.
34. Li W, Jaroszewski L, Godzik A (2001) Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 17: 282-283.
35. Inouchi A, Shinohara S, Inoue H, Kita K, Itakura M (2007) Identification of specific sequence motifs in the upstream region of 242 human miRNA genes. Comput Biol Chem 31: 207-214.
36. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190.
37. Linhart C, Halperin Y, Shamir R (2008) Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets. Genome Res 18: 1180-1189.
38. Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, et al. (2008) Ensembl 2008. Nucleic Acids Res 36: D707-714.
39. Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, et al. (2005) BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21: 3439-3440.